The Knicks are absolutely loaded with depth and talent, a rare luxury for any coach but also a curse. It is hard to find so many players meaningful minutes, much less use them all in tandem efficiently for 48 minutes. The key is to use lineups of players who are as compatible as possible to try and give everyone on the floor their best chance to make a difference offensively while not sacrificing defensive consistency. This is strictly a consideration of starting lineups. There isn't really an A unit or B unit in the NBA, players are subbed in and out more irregularly than that.
Let's consider the current starting lineup of Lin, Fields, Anthony, Stoudemire, and Chandler. Aside from Anthony and Stoudemire all of these players need to be close to the basket to really be efficient offensively. There isn't any consistent 3 point threat among any of these players, a presence that you kind of need in order to be deadly in this system. This starting unit just isn't very compatible, and apart from the anchor that Chandler provides down low it isn't very good defensively either, with Anthony and Stoudemire's troubles well-documented by now, and neither Lin nor Fields as particularly great defenders against the top guards in the league. Let's consider ways to alter the lineup without thinking of chemistry and ego and other intangibles of which we can only speculate (and which always seem to be good when the team is winning and bad when the team is losing).
My preferred starting lineup: Lin, Shumpert, Anthony, Novak, Chandler.
By replacing Fields for Shumpert, the lineup subs out a decent-to-good defender for a versatile shutdown guard. As a rookie Shumpert may be one of the best defenders in the league already, and getting major minutes in the starting unit he can wreak havoc on opposing ballhandlers and shooters, while not being the same liability Fields occasionally becomes as a result of the switch-happy team defense. On offense, Shumpert is more athletic than Landry and is likely a better finisher having accrued experience as well as recovered from his early-season knee injury. He also has decent ball-handling and facilitating ability on par with Fields', and neither are very good jump shooters. You don't lose much at all on this end of the floor while you shore up the defense dramatically.
In swapping Amar'e for Novak the team gains a 3 point shooter in the echelon of Ray Allen. Not only does he provide easy baskets when the PG finds him open behind the perimeter, but he makes everybody else better by stretching the floor for more drives in the paint, an underrated aspect of his game that players like Lin, Shumpert, and Chandler sorely need. You lose a lot of the versatility inside that Amar'e provides, but those same skills are provided by the other players already on the floor. Novak improves the spacing of the starting unit. Defensively, Novak is mediocre at best and quite poor when posted up or taken one-on-one when compared to Amar'e, but you don't really lose much otherwise simply because Amar'e is not exactly a defensive virtuoso himself. For however much Novak might drag down the defense, the benefit he provides to offense cannot be overstated and outweighs his shortcomings on the other end.
Alternately, we can consider: Lin, Shumpert, Anthony, Harrellson, Chandler.
Harrellson gives you some 3 point shooting and ability to stretch the floor like Novak, but he is far from useless on the interior and is versatile offensively. He also gives you better defense and rebounding than either of Stoudemire or Novak. I would prefer this lineup against teams with a stronger post presence. Against a team like Miami, this lineup may give the team the best chance to win.
For either of these options, Amar'e Stoudemire would become the sixth man getting major minutes off the bench, preferably entering the game for Chandler as a center who can match up against either a less energetic/backup big man. Alternatively, he can be subbed in for one of the stretch 4's while simultaneously a 3 point threat enters the game to replace the one coming out (J.R. Smith, most likely.) Assuming he returns to form a fresh Amar'e can wreak havoc on offense while his defensive shortcomings can be somewhat masked by virtue of facing less rested/talented opposition. Amar'e strikes me as very much a team player who would be willing to accept this "demotion" for the benefits it would bring to the table.
Another alternative, for those of you wary of offending any of the superstars: Lin, Smith, Anthony, Stoudemire, Chandler.
Smith gives you that outside scoring threat with some chucking tendencies that are kept in check by Lin's orchestration and Anthony/Stoudemire's usage rates. Smith can be an effective spot-up shooter from the wing/corner while bringing his athleticism and energy to defense, as well as being a 2nd ball-handler in a pinch. I get that people may prefer the Baron-Smith backcourt for chemistry or continuity reasons or what have you, but both of those guys are chuckers and you don't really want that from two of your primary ballhandlers as they are in the second unit. In this role Smith can stretch the floor for the rest of his team albeit perhaps not quite so effectively simply because he will be defended by a guard as opposed to a forward/center.
The Knicks have all the pieces to be a good team, the key is making them all fit together. It just takes some boldness and willingness to experiment.